Mechanisms and functions of RNA interference in Cryptococcus genome regulation

Epigenetic mechanisms play critical roles in adaptation of fungal pathogens through modulation of gene expression and genome stability. Key epigenetic regulators in this context are endogenous small RNA-based RNA interference (RNAi) pathways. In Cryptococcus, RNAi plays an important role in transposon regulation, with loss of RNAi causing increased rates of transposon-mediated genome variation and hence antifungal drug resistance. However, although RNAi appears to target not only transposons but also protein-coding genes in Cryptococcus, its other functions in gene regulation, and their potential roles in adaptation, remain largely unexplored. We will determine how RNAi contributes to gene regulation in response to infection-relevant environmental challenges. We will dissect both small RNA-dependent, and newly uncovered non-canonical, small RNA-independent, functions of the RNAi machinery in modulating stress resistance. Mechanistic dissection in the model C. deneoformans will be complemented by comparative analyses in other Cryptococcus species/isolates, to elucidate conservation and divergence in RNAi pathways, and determine how rewiring of the RNAi regulatory landscape contributes to diversity and adaptation. Thus, we aim to discover the mechanisms and multifaceted functions of RNAi in the context of fungal adaptation.